dvpio.read.omics.read_pg_table

dvpio.read.omics.read_pg_table(path, search_engine, *, column_mapping=None, measurement_regex=None, reader_provider_kwargs=None, **kwargs)

Read protein group table to the anndata.AnnData format

Read (features x observations) protein group matrices from proteomics search engines into the anndata.AnnData format (observations x features). Per default, raw intensities are returned, which can be modified dependening on the search engine.

Supported formats include

• AlphaDIA (alphadia)

• AlphaPept (alphapept, csv+hdf)

• DIANN (diann)

• MaxQuant (maxquant)

• Spectronaut (spectronaut, parquet + tsv)

see dvpio.read.omics.available_reader() for a complete list.

See alphabase.pg_reader module for more information

Parameters:

• path (str) – Path to protein group matrix

• reader_type – Name of engine output, pass the method name of the corresponding reader. You can list all available readers with the dvpio.read.omics.available_reader() helper function

• column_mapping (Optional[dict[str, Any]] (default: None)) – A dictionary of mapping alphabase columns (keys) to the corresponding columns in the other search engine (values). If None will be loaded from the column_mapping key of the respective search engine in pg_reader.yaml. Passed to alphabase.pg_reader.pg_reader.PGReaderProvider.get_reader().

• measurement_regex (Optional[str] (default: None)) – Regular expression that identifies correct measurement type. Only relevant if PG matrix contains multiple measurement types. For example, alphapept returns the raw protein intensity per sample in column A and the LFQ corrected value in A_LFQ. If None uses all columns. Passed to alphabase.pg_reader.pg_reader.PGReaderProvider.get_reader().

• reader_provider_kwargs (Optional[dict] (default: None)) – Passed to alphabase.pg_reader.pg_reader.PGReaderProvider.get_reader()

• kwargs (Any) – Passed to spatialdata.models.TableModel.parse()

Return type:

TableModel

Returns:

anndata.AnnData AnnData object that can be further processed with scVerse packages.

• adata.X

  Stores values of the intensity columns in the report of shape observations x features

• adata.obs

  Stores observations with protein group matrix sample names as sample_id column.

• adata.var

  Stores features and feature metadata.

Example

from dvpio.io.read.omics import read_report

alphadia_path = ...
adata = read_pg_table(alphadia_path, reader_type="alphadia")

maxquant_path = ...
# Read LFQ values from MaxQuant report
adata = read_pg_table(maxquant_path, reader_type="maxquant", measurement_regex="lfq")

Get available regular expressions

from alphabase.pg_reader import pg_reader_provider

alphapept_reader = pg_reader_provider.get_reader("alphapept")
alphapept_reader.get_preconfigured_regex()
> {'raw': '^.*(?<!_LFQ)$', 'lfq': '_LFQ$'}

See also

None